Alignments for a candidate for BPHYT_RS16930 in Bradyrhizobium sp. BTAi1

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Bradyrhizobium sp. BTAi1

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_012046028.1 BBTA_RS28795 sugar ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_000015165.1:WP_012046028.1
          Length = 500

 Score =  377 bits (969), Expect = e-109
 Identities = 214/494 (43%), Positives = 314/494 (63%), Gaps = 7/494 (1%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L   +IGK +PGV ALD VS  V  G+V  L+GENGAGKSTL+++LGG   P SG + ID
Sbjct: 6   LELIDIGKTYPGVVALDHVSLSVAPGEVVALLGENGAGKSTLMRVLGGVVAPSSGTIRID 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP---NSLGWVNKREAKRFV 121
           G      S A +IAAGIA +HQEL    +L VA N+ +G+ P     L  ++++     V
Sbjct: 66  GVARTSYSVADAIAAGIAFVHQELNLFDNLDVAGNVFIGREPVHGGLLKLIDRKTLLAKV 125

Query: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181
           R  ++ +G    P+  L +LS+AQRQ+VEI KAL  +AR + +DEPTSSL+  ETE L +
Sbjct: 126 RPLIDRLGADFAPDTPLAELSLAQRQLVEIIKALSLDARCVIMDEPTSSLTLSETERLMQ 185

Query: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241
           ++  L+AD  ++I+I+HR++E+ +  D   + RDGR + +  T E +    ++  M+GR+
Sbjct: 186 VIAGLKADGVSVIFITHRLNEVMQCADHAIVLRDGRMVGA-LTREELNPAAMIRLMIGRD 244

Query: 242 ISDIYNYSARPLGE-VRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300
           +  +Y   A P GE +   A  +      Q  S ++RRGEI+G  GLVGAGR+EL   ++
Sbjct: 245 LRSLYVPPAAPPGETILDVADAVTSTYPHQAVSLQLRRGEILGLAGLVGAGRTELARAIF 304

Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360
           G D    G + +DG+PI++ S  EAI  GI L PEDRK  G++   ++++N+++     Y
Sbjct: 305 GVDPLLAGGISVDGEPIRIASPREAIDRGIYLIPEDRKACGLLLELSMAQNVSLPDLASY 364

Query: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 420
              G+ +D  +E   AD   + LKI+    +  +  LSGGNQQK +L++WL+    KV+I
Sbjct: 365 SSFGL-VDTVRETANADHQRERLKIRAADVKAPVGTLSGGNQQKVVLAKWLSMRP-KVLI 422

Query: 421 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT 480
            DEPTRGIDVGAK EIY+++ +L++ G AI+MISS++ EV+GVSDRI VM +GRISG L 
Sbjct: 423 FDEPTRGIDVGAKQEIYDMLRRLSDAGVAILMISSDMEEVIGVSDRIAVMHEGRISGFLA 482

Query: 481 RKDATEQSVLSLAL 494
           R + +E +VL LA+
Sbjct: 483 RSEFSEHNVLQLAV 496



 Score = 72.8 bits (177), Expect = 3e-17
 Identities = 67/254 (26%), Positives = 109/254 (42%), Gaps = 13/254 (5%)

Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311
           P  E+    K   G       S  V  GE+V   G  GAG+S LM ++ G      G + 
Sbjct: 4   PFLELIDIGKTYPGVVALDHVSLSVAPGEVVALLGENGAGKSTLMRVLGGVVAPSSGTIR 63

Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRK- 370
           +DG      S  +AI  GI       +E  +     V+ N+ I     +  +   +DRK 
Sbjct: 64  IDGVARTSYSVADAIAAGIAFV---HQELNLFDNLDVAGNVFIGREPVHGGLLKLIDRKT 120

Query: 371 ---KEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRG 427
              K     DR        TP     +  LS   +Q   + + L+  D + VI+DEPT  
Sbjct: 121 LLAKVRPLIDRLGADFAPDTP-----LAELSLAQRQLVEIIKALSL-DARCVIMDEPTSS 174

Query: 428 IDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQ 487
           + +     +  VI  L   G +++ I+  L EV+  +D  +V+R GR+ G LTR++    
Sbjct: 175 LTLSETERLMQVIAGLKADGVSVIFITHRLNEVMQCADHAIVLRDGRMVGALTREELNPA 234

Query: 488 SVLSLALPQSSTAL 501
           +++ L + +   +L
Sbjct: 235 AMIRLMIGRDLRSL 248


Lambda     K      H
   0.320    0.136    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 626
Number of extensions: 32
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 500
Length adjustment: 34
Effective length of query: 478
Effective length of database: 466
Effective search space:   222748
Effective search space used:   222748
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources